The Fallout 3 Mothership Zeta Looks awesome

Well, I read two separate reports on the issue, contrary to you information.

1) You can get the DLC, which is in a specific folder and move it to the Fallout directory in steam. Here basically the issue is that the DLC's are not in a place that F3 will recognize because Steam installs all games in a specific folder.

2) That I cannot corroborate at the moment, but I read a new patch specific for the Steam version allows to recognize the folder of the DLC content in case you get them from Windows Live.

 

The Steam version of Fallout3 will recognize the DLCs if you log into Games for Windows Live, even an "offline" profile. If you don't want to use GfWL, you can download the DLC and copy the files to the FO3 data folder (if you have DLC and use the Fallout Mod Manager, the Mod Manager will ask if you want to move your DLC to the FO3 data folder)

I don't know about any sort of Steam-only patch; All patches are either downloaded from bethsoft.com, or the game is updated through the GfWL toolbar system. Steam has nothing to do with patches for FO3. Steam actually has pretty much nothing to do with the way FO3 runs at all, actually. If you launch FO3 from it's main "fallout3.exe" file, it will completely bypass Steam, you don't get the Steam "Preparing to launch <game>" window, and you don't even actually need Steam running at all!

To me, it looks like the Steam version is basically the disc version, downloaded through Steam, not a special Steam version.